SARS-CoV-2 Disease Severity and Cycle Threshold Values in Children Infected during Pre-Delta, Delta, and Omicron Periods, Colorado, USA, 2021–2022

In adults, viral load and disease severity can differ by SARS-CoV-2 variant, patterns less understood in children. We evaluated symptomatology, cycle threshold (Ct) values, and SARS-CoV-2 variants among 2,299 pediatric SARS-CoV-2 patients (0–21 years of age) in Colorado, USA, to determine whether children infected with Delta or Omicron had different symptom severity or Ct values than during earlier variants. Children infected during the Delta and Omicron periods had lower Ct values than those infected during pre-Delta, and children <1 year of age had lower Ct values than older children. Hospitalized symptomatic children had lower Ct values than asymptomatic patients. Compared with pre-Delta, more children infected during Delta and Omicron were symptomatic (75.4% pre-Delta, 95.3% Delta, 99.5% Omicron), admitted to intensive care (18.8% pre-Delta, 39.5% Delta, 22.9% Omicron), or received oxygen support (42.0% pre-Delta, 66.3% Delta, 62.3% Omicron). Our data reinforce the need to include children, especially younger children, in pathogen surveillance efforts.


Bioinformatic analysis of whole genome sequencing data
All of our bioinformatics workflows were written in WDL (Workflow Development Language), are compatible with Google Cloud and the Broad Institute's terra.bioplatform (4), and have been made publicly available on github (5) and dockstore (6).For samples sequenced on ONT GridION, quality filtering and trimming of reads and reference-guided assembly were performed using our nanopore-preprocessing-assembly.wdlworkflow.For samples sequenced on Illumina NextSeq, quality filtering and trimming of reads and reference-guided assembly were performed using our COVIDseqSEassembly.wdlworkflow.Lineage assignment was performed on all resulting consensus genome assemblies using our classifyCOVIDlineage.wdl, which uses NextClade and Pangolin to assign clade and lineage information.Among sequenced samples, we obtained a mean base quality of 29.4 (SD 6.6), mean number of filtered reads per sample of 392,256.01 (SD 397,572.6),mean sequencing depth of 1013.2 (SD 719.6), mean mapping quality of 59.9 (SD 0.4), and mean percent reference coverage of 94.3 (SD 7.8).All sequenced samples with at least 50% coverage were made publicly available on GISAID and NCBI (Table S1).

Table 1 .
6. Colorado Department of Public Health and Environment.CDPHEsarscov2 [cited 2022 Feb 22].https://dockstore.org/organizations/CDPHE/collections/CDPHEsarscov2.NCBI and GISAID accession IDs for all samples that were successfully sequenced to at least 50% reference genome coverage and submitted to public repositories

Table 6 .
Values are no.(%) [95% CI] except as indicated.†P values were obtained from χ 2 test of patient characteristics across the 3 variant periods.‡Unknown racial-ethnic group includes individuals with unknown, unknown or not reported, or missing race or ethnicity variables.NH = Non-Hispanic.§Any comorbidity includes past medical history of cardiac, respiratory, gastrointestinal/liver, neurologic, oncologic, obesity, chronic kidney disease, diabetes, or other comorbid condition.Statistical analysis of N gene Ct values are response variables and predictor variables of time frame, race/ethnicity group, age bin, sex, days between symptom onset and test (onset_days_bin), patient type (includes outpatient, inpatient with COVID-19, and inpatient due to COVID-19), vaccination status, symptoms, hospital stay duration, comorbidity, PICU admission, and receipt of oxygen support* Predictor variables and covariates are separated by a colon.While all possible pairwise comparisons were performed within data categories across variant periods, comparisons considered in this study include those between categories but within variant period (e.g., age groups within Delta) and the same category across variant periods (e.g., 1-4 y olds across pre-Delta, Delta, and Omicron).As such, comparisons not relevant to the current study were not included in post-hoc test ✝✝ (e.g., 12+ years during Omicron vs. <1 y during Delta).Ct, cycle threshold; N, nucleocapsid; PICU, pediatric intensive care unit.✝Significance codes: 0.001 '***', 0.01 '**', 0.05 '*', 0.1 '.', 1 ' '. ǂInpatient because of COVID-19.§Two-way ANOVA unless otherwise noted, ANOVAs were followed up with post-hoc Tukey HSD, p values from post-hoc tests are presented in the figures and text. **

Table 7 .
Statistical analysis of N gene Ct values are response variables and predictor variables of sequenced lineage, race/ethnicity group, age bin, sex, days between symptom onset and test (onset_days_bin), patient type (includes outpatient, inpatient with COVID-19, and inpatient due to COVID-19), vaccination status, symptoms, hospital stay duration, comorbidity, PICU admission, and receipt of oxygen support* Predictor variables and covariates are separated by a colon.While all possible pairwise comparisons were performed within data categories across lineage groups, comparisons considered in this study include those between categories but within lineage group (e.g., age groups within Delta) and the same category across variant periods (e.g., 1-4 y olds across Other, Delta, and Omicron).As such, comparisons not relevant to the current study were not included in post-hoc test ✝✝ (e.g., 12+ years during Omicron vs. <1 y during Delta).Ct, cycle threshold; N, nucleocapsid; PICU, pediatric intensive care unit.✝Significancecodes: 0.001 '***', 0.01 '**', 0.05 '*', 0.1 '.', 1 ' '.ǂInpatient DUE to COVID-19 §Two-way ANOVA unless otherwise noted, ANOVAs were followed up with post-hoc Tukey HSD, p values from post-hoc tests are presented in the figures and text. *

Table 8 .
Mean nucleocapsid gene cycle threshold values (+SD) by category